Emulator

Game Name?
The Legend of Zelda (Collector's Edition version)

Possibly other NES games as well.

Game ID?
PZLE01

What's the problem? Describe what went wrong in few words.
Enabling progressive scan (hold B while game boots) doesn't seem to fix the graphical glitches in the game, at least on my system. Enabling RealXFB does fix the graphical glitches, but it is not enabled by default in the game ini.

What steps will reproduce the problem?

1. Load game with default settings

Which versions of Dolphin did you test on?
4.0-4091

Does using an older version of Dolphin solve your issue? If yes, which
versions of Dolphin used to work?
No.

What are your PC specifications?
Windows 7 Professional 64-bit SP1
Intel Core i3 2120 @ 3.30GHz
4.00GB Dual-Channel DDR3
Intel Corporation DZ68DB
2047MB NVIDIA GeForce GTX 650 (PNY)

Is there any other relevant information?
The game looks as it does at https://dolphin-emu.org/m/user/blog/progress-report/september-2014/zelda-collectors-edition-broken.png by default, even when holding B while starting up the game as instructed (and progressive scan is enabled in the INI, I haven't screwed with anything). I guess I should mention I'm holding B on the configured GCN controller.

Proposed fix
Add the following lines to dolphin/Data/Sys/GameSettings/PZLE01.ini to enable RealXFB by default on the title. Possibly remove progressive scan and the line about it from the game ini as well if it's not needed.
UseXFB = True
UseRealXFB = True